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Abstract Boletellu s and Aureoboletus are among the most prominent bolete genera in the family Boletaceae . The diversity of these taxa in the Caribbean is high, but their species delimitation is still critical. An inclusive phylogenetic reconstruction of these genera is achieved by sequencing five loci: nuclear ribosomal DNA regions (ITS, LSU) and protein coding genes ( TEF 1-α, RPB 1, and RPB 2). Three target species from the Greater Antilles of the Caribbean (Dominican Republic and Puerto Rico) are included in the analysis. The phylogenetic position of these critical taxa is assessed and discussed. Accurate macro- and micromorphological descriptions are provided for Boletellus ananas , B. cubensis , and B. domingensis , accompanied by line drawings of their main microscopical features. Boletellus cubensis is documented in detail for the first time from the Dominican Republic and Puerto Rico. Moreover, DNA sequences are successfully generated from isotype specimens of the South American Boletellus exiguus (ITS), B. piakaii (ITS), the Australian B. reminiscens (ITS), and B. sinapipes (ITS), as well as from single specimens of the African B. rubrolutescens (ITS) and B. sinochrysenteroides (ITS, LSU, and TEF 1-α) from Far Eastern Russia (the first record for that country) and integrated in the phylogeny. Several accessions of five gene markers (ITS, LSU, TEF 1-α, RPB 1, and RPB 2) from five different collections of an unnamed Aureoboletus species from Guatemala (Mesoamerica) have also been added to the dataset. In addition, type collections of the 178-year-old material of B. ananas and of the infraspecific taxa B. coccineus var. amarus and B. ananas var. crassotunicatus are microscopically re-examined, and a revision of their microscopic data is provided. A full description of a couple of recent Australian collections of Boletellus cf. emodensis is also supplemented as extralimital materials. This study confirms the Caribbean as a hotspot for Boletaceae diversity, with the potential to fill many gaps in the global evolutionary history of this family. Our phylogenetic outcomes point towards the need for a genus-wide, revised classification of Boletellus and Aureoboletus , which is aimed at resolving higher-level infrageneric relationships. However, our results also show that it is still premature to split these potentially polyphyletic genera into smaller units, as long as a more extensive knowledge on critical taxa is lacking and species sampling is incomplete.